Pseudogenes in the Matrix

Over at BioLogos, Dennis Venema and Darrel Falk have written a nice summary of pseudogenes and how they relate to our understanding of common descent. But we can take their discussion to a deeper level to help you better appreciate pseudogenes from a teleological perspective.

Where do pseudogenes come from? By definition, they are copies of previously existing genes that are now under a process of genomic decay. We can thus think of pseudogenes as the off-shoot of DNA processing mechanisms. Genes are duplicated in a protein-dependent manner, whether it be through recombination, nondisjunction, or retroposition. As far as I know, gene copies do not originate without molecular machines that mediate these interactions.

Now, it is common to think of such change as a “mistake” or “error.” But another way to look at it is that genomes are constantly being processed in a manner such that they are sending out “feelers” into the environment to test possible upgrades. As such, a pseudogene is not a mistake, it is simply a solution that was not needed and is thus being discarded. Cells and genomes rely on feelers, not foresight. The pseudogene itself is not a product of design, but may be the off-shoot of an intelligently designed search process.

In fact, in The Design Matrix, I argue that gene duplication (a process that can generate pseudogenes), is precisely a mechanism we would expect to exist from the perspective of front-loading evolution:

Gene duplication solves the design problems cited above simply because cells can retain the core designed state while the duplicate is free to mutate and explore new solutions. As long as the original is effectively retained, the pathway to the new function is retained and propagated. It is a beautiful solution for a front-loading designer. In one process, we both propagate the original design and set things up to unpack secondary designs without erasing the original design. Stability and change, all in one package. As an added bonus, the influence of contingency is dampened. It does not matter if some or many gene duplication events drift off in unintended fashion (most will merely tweak the original function or decay away). The beauty of gene duplication is that it explores sequence space while retaining and propagating the original sequence. As long as the original sequence is essentially retained somewhere, someplace, evolution gets to “try again” over and over and over in its rigged search for some future design. In other words, if a designer wanted a secondary design to unpack itself in an animal cell, duplication of the original sequence is bound to happen in all cells, including animal cells. When it eventually occurs in an animal cell, the stage is set to unpack the secondary design. If it fails, we need only wait until the next round of duplication and mutation occurs. It is the intelligent use of chance.

So while most are content to view gene duplication and pseudogenes merely as a sign of common descent, there is a deeper perspective available that will help you to begin to appreciate the logic of evolution.

I might also propose two other frontloading possibility to pseudogenes. It may have been a very simple archaic way of increasing size to multi-cell organisms. Pseudogenes might also be part of archaic, no longer needed, alternate expression in multiple cell types within the same organism. They might have been necessary steps to a more refined process of gene regulation.